Select the groups that will be analysed: Primary solid Tumor and Solid Tissue Normal.

![](figures/elmer_analysis_groups.png)

We will identify probes that are hypomethylated in Primary solid Tumor compared to Solid Tissue Normal.

![](figures/elmer_analysis_diffmeth.png)

For the significant differently methylated probes identified before we will correlated
with the 20 nearest genes. Change the value of the field `Number of permutations` to `100`,
`Raw P-value cut-off` to `0.05` and `Empirical P value cut-off` to `0.01`.

![](figures/elmer_analysis_pair.png)

There will be no changes in the step 3.

![](figures/elmer_analysis_motif.png)

There will be no changes in the step 4.

![](figures/elmer_analysis_TF.png)

Click on `Run the analysis`.

![](figures/elmer_analysis_final.png)

If the analysis identified significant regulatory TF the results will be saved into an R object.

![](figures/elmer_analysis_message.png)
## Visualize results

To visualize the results go to `Integrative analysis/ELMER/Visualize results`.

![](figures/elmer_visualize_results.png)

Click on `Select results` and select the object created on the previous section.

You will be able to visualize the correlation between
DNA methyation levels and gene expression selecting a pair of gene and probe.

![](figures/elmer_visualize_plot_scatter_byPair.png)

A probe and its near genes.

![](figures/elmer_visualize_plot_scatter_byProbe.png)

Or the avarage DNA methylation levels of probes of a Motif vs the expression of a
TF.

![](figures/elmer_visualize_plot_scatter_byTF.png)

For each enriched motif you can verify the ranking of sigificances between the correlation
of DNA methylation level on the significant paired probes with that motif vs the TF expression (for all human TF).

![](figures/elmer_visualize_tfraningplot.png)

The enrichement of each motif can be visualized.

![](figures/elemer_visualize_motif_enrichment.png)

You can take a look for a gene which was the probe linked.

![](figures/elemer_visualize_schematic_gene.png)

You can see the plot and its neraby genes.

![](figures/elemer_visualize_schematic_probe.png)

It is possible to visualize the table with the significant differently methylated probes.

![](figures/elmer_visualize_table_sigprobes.png)

It is possible to visualize the table with the pairs genes probes that have an negative correlation between
DNA methyation levels and gene expression.

![](figures/elmer_visualize_table_pair.png)

It is possible to visualize the table with the enriched motifs.

![](figures/elmer_visualize_table_enriched_motif.png)

It is possible to visualize the table with the candidates regulatory TF.